Structure of PDB 8dat Chain G Binding Site BS02

Receptor Information
>8dat Chain G (length=474) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RYGPLRIKELAVDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDK
EYHEKNKIKHISFHSYLKKLNENANKKENGSSYISPLSEPDFRINKRCHN
GHEPWPRGICSKCQPSAITLQQQEFRMVDHVEFQKSEIINEFIQAWRYTG
MQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMDVEQVKNE
MLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVI
MAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAE
ALVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPA
FPVDYLLVTLTHGFPNTDTETNSKFVSSTGFPWSNRQAMGQSQDYQELKK
YLFNVASSGDFNLLHEKISNFHLLLYINSLQILSPDEWKLLIESAVKNEW
EESLLKLVSSAGWQTLVMILQESG
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain8dat Chain G Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8dat SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		C204 H208 C216 C219
Binding residue
(residue number reindexed from 1)		C98 H102 C110 C113
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0031625 ubiquitin protein ligase binding
GO:0036435 K48-linked polyubiquitin modification-dependent protein binding
GO:0043130 ubiquitin binding
Biological Process
GO:0006274 DNA replication termination
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006515 protein quality control for misfolded or incompletely synthesized proteins
GO:0015031 protein transport
GO:0030970 retrograde protein transport, ER to cytosol
GO:0036503 ERAD pathway
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0051028 mRNA transport
GO:0051228 mitotic spindle disassembly
GO:0070651 nonfunctional rRNA decay
GO:0071629 cytoplasm protein quality control by the ubiquitin-proteasome system
GO:0072344 rescue of stalled ribosome
GO:0072665 protein localization to vacuole
GO:0072671 mitochondria-associated ubiquitin-dependent protein catabolic process
GO:0099638 endosome to plasma membrane protein transport
GO:1900182 positive regulation of protein localization to nucleus
GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process
Cellular Component
GO:0000837 Doa10p ubiquitin ligase complex
GO:0000839 Hrd1p ubiquitin ligase ERAD-L complex
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0030894 replisome
GO:0031965 nuclear membrane
GO:0034098 VCP-NPL4-UFD1 AAA ATPase complex
GO:0036266 Cdc48p-Npl4p-Vms1p AAA ATPase complex
GO:0042175 nuclear outer membrane-endoplasmic reticulum membrane network
GO:0048471 perinuclear region of cytoplasm
GO:1990112 RQC complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8dat, PDBe:8dat, PDBj:8dat
PDBsum8dat
PubMed36574706
UniProtP33755|NPL4_YEAST Nuclear protein localization protein 4 (Gene Name=NPL4)

[Back to BioLiP]